Sharon Browning and colleagues published a paper in Cell last week that shows there are uniquely different Denisovan genomes in the DNA of East Asian individuals, indicating that interbreeding with Homo sapiens happened in two independent episodes. See we already knew Aboriginal genomes from Australia and Papua New Guinea contain fragments of Denisovan DNA. Introgression of Denisovans is nothing new, but this a second Denisovan ancestry was not found in these populations. And that’s the exciting thing about this study.
Browning and crew compared 5,639 whole genome sequences from people who live in Europe, Asia, Oceania, and the Americas to the known Altai Siberian Denisovan genome. They got their samples from UK10K Project, 1000 Genomes Project, and the Simons Genome Diversity Project. They noticed that the Aboriginal Denisovans matched to the true Siberian Denisovan genome. People of South Asian and Oceanian descent had different sets of Denisovan genes from people of East Asian descent. Denisovan genes in the eastern populations, such as the Han Chinese, Chinese Dai, and Japanese were more closer. In other words, people of South Asian and Oceanian had different sets of Denisovan genes from East Asians.
This allows them to make the conclusion that two distinct Denisovan populations mated with humans. Both of these populations mated with the ancestors of East Asians, but one population mated with the ancestors of South Asians and Oceanians. A plausible scenario is that as the first Denisovans split within Eurasia, some moved towards Siberia while others towards Oceania. Around 40-60,000 years ago, modern humans were migrating all over, interbreeding without human populations. Just how exactly this happened is uncertain. But I can say with confidence based on studies like this that Denisovan DNA introgressed at least twice because the species ranged widely throughout Asia.